Serine proteases: Evolutionary trees

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Catalog	Fitch/89	Fitch/extended
Taxonomy	Kitch/89	Kitch/extended
Tree of Life	PileUp/89	PileUp/extended

Phylogenic tree of S1 serine proteases, Fitch-Margoliash method, 89 sequences

A phylogenetic tree of 89 S1 serine proteases was built by Krem et al. (1999, JBC, in press) from residues 16 to 245 according to the chymotrypsin numbering. Original sequences were culled from GenBank. 89 non-redundant sequences were selected and aligned by Clustal-W 1.7. Protein distance matrices were calculated with PROTDIST from the PHYLIP package. Unrooted trees were built using the Fitch-Margoliash method with the PHYLIP program FITCH 3.572c. Distances from PRODIST are available here.

1	Display 1 position through the tree Enter the position according to chymotrypsin numbers and click view to perform.

Display up to 10 positions on the left of the tree
You can choose up to 10 positions for displaying the amino-acid distribution through the evolutionary tree. Positions are not necessarly contiguous.
Enter the number of positions (10 max) and the list of position numbers according to chymotrypsin used as reference (numbers have to be separated by space on the same line). Click the "Analyse" button to perform the application.The corresponding positions of every sequence are displayed on the left of the tree keeping the order of the request.
Example: 5 - 225 226 227 57 189
-
Result of example, first line: PFYKDXXXXX ! +------ chymomosq

Display of conservative residues over a sequence, a 2D structure sketch or a 3D structure
Choose the level of the output display:
results are displayed in tables
selected sequences are color-coded
secondary structure sketches of selected sequences are color-coded
peptidic skeleton of one 3D-structure is color coded in a Rasmol window
van der Waals surface of one 3D-structure is color coded in a Rasmol window.
Select for every sequence in the tree (on the right of sequence names) if residues have to be strictly identical (I), similar (S) or different (D). By default all sequences are not selected (O).
At least one sequence has to be selected in the identical set (I). If you select at least one sequence in the similar set (S), choose the appropriate substitution matrix and threshold .
Click to open a window with the results. Click to initialize by default.

 
  POSITIONS     FITCH-MARGOLIASH UNROOTED TREE (Krem et al.,1999, JBC, in press) 
 1234567890 Sequence names are linked to SwissProt. Numbers are knot references in the distance list.



 XXXXXXXXXX  +-- chymoshrmp (S1)  I  S  D  O
             ! 
 XXXXXXXXXX  !          +------ chymomosq (S1)  I  S  D  O
             !       +-69 
 XXXXXXXXXX  !       !  +------- ser1fly (S1)  I  S  D  O
             !       ! 
 XXXXXXXXXX  !       !  +----- factorD (S1)  I  S  D  O
             !       !  ! 
 XXXXXXXXXX  !       !  !        +-- chymase (S1)  I  S  D  O
             !    +-59  !     +-33  
 XXXXXXXXXX  !    !  !  !     !  !  +-- MCP-like (S1)  I  S  D  O
             !    !  !  !     !  +-32  
 XXXXXXXXXX  !    !  !  !     !     +-- MCP-1 (S1)  I  S  D  O
             !    !  !  !     !  
 XXXXXXXXXX  !    !  !  !     !            +-- granzymeF (S1) I  S  D  O
             !    !  !  !     !        +--30  
 XXXXXXXXXX  !    !  +-57     !        !   +-- granzymeD (S1)  I  S  D  O
             !    !     !     !        !  
 XXXXXXXXXX  !    !     !  +-31        !                         +------------------------- proteaseC (S2A)  I  S  D  O
             !    !     !  !  !     +-26                      +-76   
 XXXXXXXXXX  !    !     !  !  !     !  !                      !  +----- granz-l-II (S1)  I  S  D  O
             !    !     !  !  !     !  !   +----------------25  
 XXXXXXXXXX  !    !     !  !  !     !  !   !                  !                   +-- proteaseA (S2A)  I  S  D  O
             !    !     !  !  !     !  !   !                  !                +-52   
 XXXXXXXXXX  !    !     !  !  !  +-27  +--51                  +---------------53  +---- proteaseD (S2A)  I  S  D  O
             !    !     !  !  !  !  !      !                                   !   
 XXXXXXXXXX  !    !     !  !  !  !  !      !                                   +-- proteaseB (S2A)  I  S  D  O
             !    !     +-24  !  !  !      !  
 XXXXXXXXXX  !    !        !  +-29  !      +-- MCP-8 (S1)  I  S  D  O
             !    !        !     !  !  
 XXXXXXXXXX  !    !        !     !  +--- cathepsinG (S1)  I  S  D  O
             !    !        !     !  
 XXXXXXXXXX  !    !        !     !  +-- NKCP-1 (S1)  I  S  D  O
             !    !        !     +-28  
 XXXXXXXXXX  !    !        !        +-- granzymeB (S1)  I  S  D  O
             !    !        !  
 XXXXXXXXXX  !    !        !  +------ granzymeA (S1)  I  S  D  O
             !    !        +-58  
 XXXXXXXXXX  !    !           !   +--- pmn-elasta (S1)  I  S  D  O
             !    !           +--22  
 XXXXXXXXXX  !    !               !  +----- azurocidin (S1)  I  S  D  O
             !    !               +-23   
 XXXXXXXXXX  !    !                  +--- myeloblast (S1)  I  S  D  O
             !    !  
 XXXXXXXXXX  !    !     +-------------------------------  Nsp4-EAV (?)  I  S  D  O
             !    !  +-86  
 XXXXXXXXXX  !    !  !  !        +----- scatter (S1)  I  S  D  O
             !    !  !  +-------37  
 XXXXXXXXXX  1---21  !           +----- HGF-like (S1)  I  S  D  O
             !    !  !  
 XXXXXXXXXX  !    !  !        +------------------ cercarial (S1)  I  S  D  O
             !    !  !        !  
 XXXXXXXXXX  !    !  !     +-38   +---- SCCE (S1)  I  S  D  O
             !    !  !     !  !   !   
 XXXXXXXXXX  !    !  !     !  !   !        +-- kallikrein (S1)  I  S  D  O
             !    !  !     !  +--17     +-13  
 XXXXXXXXXX  !    !  !     !      !  +-15  +-- PSA (S1)  I  S  D  O
             !    !  !     !      !  !  !  
 XXXXXXXXXX  !    !  !     !      +-14  +-- Resterase (S1)  I  S  D  O
             !    !  !     !         !  
 XXXXXXXXXX  !    !  !     !         !  +-- tonin (S1)  I  S  D  O
             !    !  !     !         +-16  
 XXXXXXXXXX  !    !  !     !            +--- g-renin (S1)  I  S  D  O
             !    !  !     !  
 XXXXXXXXXX  !    !  !     !                 +-- plasmin (S1)  I  S  D  O
             !    !  !     !           +----35  
 XXXXXXXXXX  !    !  !     !           !     +-- apolipo-A (S1)  I  S  D  O
             !    !  !     !           !  
 XXXXXXXXXX  !    !  !     !           !  +--------- factorI (S1)  I  S  D  O
             !    !  !     !           !  !  
 XXXXXXXXXX  !    !  !     !        +-36  !       +-- elastase2 (S1)  I  S  D  O
             !    !  !     !        !  !  !  +---39  
 XXXXXXXXXX  !    !  !     !        !  !  !  !    +--- caldecrin (S1)  I  S  D  O
             !    !  !     !        !  !  !  !  
 XXXXXXXXXX  !    !  !     !        !  !  !  !        +----- u-PA (S1)  I  S  D  O
             !    !  !     !        !  +-74  !     +--5  
 XXXXXXXXXX  !    !  !     !        !     !  !     !  !   +-- t-PA (S1)  I  S  D  O
             !    !  !     !        !     !  !     !  +---4  
 XXXXXXXXXX  !    !  !     !        !     !  !     !      +-- s-PA (S1)  I  S  D  O
             !    !  !     !        !     !  !  +--6   
 XXXXXXXXXX  !    !  !     !        !     !  !  !  !            +------ C2 (S1)  I  S  D  O
             !    !  !     !        !     !  !  !  !  +--------84  
 XXXXXXXXXX  !    !  !     !        !     !  !  !  !  !         +------- factorB (S1)  I  S  D  O
             !    !  !     !        !     +-63  !  +-83  
 XXXXXXXXXX  !    !  !     !        !        !  !     !  +---- HGFA (S1)  I  S  D  O
             !    !  !     !        !        !  !     +--2  
 XXXXXXXXXX  !    !  !     !        !        !  !        +---- factorXII (S1)  I  S  D  O
             !    !  !     !        !        !  !  
 XXXXXXXXXX  !    +-34     !        !        !  !     +--------- easter (S1)  I  S  D  O
             !       !     !        !        !  !  +-78  
 XXXXXXXXXX  !       !     !        !        !  !  !  +--------- SP24Dmosq (XX)  I  S  D  O
             !       !     !        !        !  !  !  
 XXXXXXXXXX  !       !     !        !        !  !  !                 +----- trypStrep (S2A)  I  S  D  O
             !       !     !        !        !  !  !              +-62  
 XXXXXXXXXX  !       !     !        !        !  !  !              !  +--- trypFoxy (S1)  I  S  D  O
             !       !     !        !        !  !  !           +-61  
 XXXXXXXXXX  !       !     !        !        +-47  !           !  !  +----------------- Elegans208 (XX)  I  S  D  O
             !       !  +--8        !           !  !           !  !  !  
 XXXXXXXXXX  !       !  !  !        !           !  !           !  +-85  +-------- nudel (S1)  I  S  D  O
             !       !  !  !        !           !  !           !     !  !  
 XXXXXXXXXX  !       !  !  !        !           !  !           !     +-70  +------ stubble (S1)  I  S  D  O
             !       !  !  !        !           !  !           !        !  !  
 XXXXXXXXXX  !       !  !  !        !           !  !           !        +-64  +----------- snake (S1)  I  S  D  O
             !       !  !  !        !           !  !           !           !  !  
 XXXXXXXXXX  !       !  !  !        !           !  !           !           !  !     +---- trypsinfly (S1)  I  S  D  O
             !       !  !  !        !           !  !           !           +-79  +-46  
 XXXXXXXXXX  !       !  !  !        !           !  !           !              !  !  !  +-- hypodermB (S1)  I  S  D  O
             !       !  !  !        !           !  !        +-75              !  !  +-45  
 XXXXXXXXXX  !       !  !  !     +-42           !  !        !  !              +-44     +-- hypodermA (S1)  I  S  D  O
             !       !  !  !     !  !           !  !        !  !                 !   
 XXXXXXXXXX  !       !  !  !     !  !           !  !        !  !                 !  +------ vitellin (S1)  I  S  D  O
             !       !  !  !     !  !           !  !        !  !                 +-60   
 XXXXXXXXXX  !       !  !  !     !  !           !  !        !  !                    !    +-- allergen2 (S1)  I  S  D  O
             !       !  !  !     !  !           +-71        !  !                    +---43   
 XXXXXXXXXX  !       !  !  !     !  !              !        !  !                         +-- allergen1 (S1)  I  S  D  O
             !       !  !  !     !  !              !        !  !  
 XXXXXXXXXX  !       !  !  !     !  !              !        !  !     +------- proteinC (S1)  I  S  D  O
             !       !  !  !     !  !              !        !  !  +-67  
 XXXXXXXXXX  !       !  !  !     !  !              !        !  !  !  +------ factorIX (S1)  I  S  D  O
             !       !  !  !     !  !              !        !  !  !  
 XXXXXXXXXX  !       !  !  !     !  !              !        !  +-68     +--------- Elegans157 (XX)  I  S  D  O
             !       !  !  !     !  !              !        !     !  +-56  
 XXXXXXXXXX  !       !  !  !     !  !              !        !     !  !  +------ factorVII (S1)  I  S  D  O
             !       !  !  !     !  !              !     +-40     +-82  
 XXXXXXXXXX  !       !  !  !     !  !              !     !  !        !  +-------- Elegans132 (XX)  I  S  D  O
             !       !  !  !     !  !              !     !  !        !  !   
 XXXXXXXXXX  !       !  !  !     !  !              !     !  !        +-50     +------ MASP-1 (S1)  I  S  D  O
             !       !  !  !     !  !              !     !  !           !  +-73  
 XXXXXXXXXX  !       !  !  !     !  !              !     !  !           !  !  +----- clotfactC (S1)  I  S  D  O
             !       !  !  !  +-87  !              !     !  !           +-72  
 XXXXXXXXXX  !       !  !  !  !  !  !              !     !  !              !  +------ MASP-2 (S1)  I  S  D  O
             !       +-12  !  !  !  !              !     !  !              !  !   
 XXXXXXXXXX  !          !  !  !  !  !              !  +-77  !              +-66     +-------- haptoglobin (?)  I  S  D  O
             !          !  !  !  !  !              !  !  !  !                 !  +-80  
 XXXXXXXXXX  !          !  !  !  !  !              !  !  !  !                 !  !  !    +-- C1s (S1)  I  S  D  O
             !          !  !  !  !  !              !  !  !  !                 +-49  +---48  
 XXXXXXXXXX  !          !  !  !  !  !              !  !  !  !                    !       +-- CASP (S1)  I  S  D  O
             !          !  !  !  !  !              !  !  !  !                    !   
 XXXXXXXXXX  !          !  !  !  !  !              +-54  !  !                    +------ C1r (S1)  I  S  D  O
             !          !  !  !  !  !                 !  !  !  
 XXXXXXXXXX  !          !  !  !  !  !                 !  !  +------- thrombin (S1)  I  S  D  O
             !          !  !  !  !  !                 !  !  
 XXXXXXXXXX  !          !  !  !  !  !                 !  +------- proclottin (S1)  I  S  D  O
             !          !  +--3  !  !                 !   
 XXXXXXXXXX  !          !     !  !  !                 +------- factorX (S1)  I  S  D  O
             !          !     !  !  !  
 XXXXXXXXXX  !          !     !  !  !  +-- chymo-lhum (S1)  I  S  D  O
             !          !     !  !  +-41  
 XXXXXXXXXX  !          !     !  !     +-- chymohuman (S1)  I  S  D  O
             !          !     !  !  
 XXXXXXXXXX  !          !     !  +------ tryptase (S1)  I  S  D  O
             !          !     !   
 XXXXXXXXXX  !          !     !     +----- prostasin (S1)  I  S  D  O
             !          !     !     !  
 XXXXXXXXXX  !          !     !  +-55     +------ acrosin (S1)  I  S  D  O
             !          !     !  !  !  +-65  
 XXXXXXXXXX  !          !     !  !  !  !  +---- hepsin (S1)  I  S  D  O
             !          !     !  !  +-10  
 XXXXXXXXXX  !          !     +--7     !   +-- p-kallikre (S1)  I  S  D  O
             !          !        !     +---9  
 XXXXXXXXXX  !          !        !         +-- factorXI (S1)  I  S  D  O
             !          !        !  
 XXXXXXXXXX  !          !        +----- enterokina (S1 I  S  D  O
             !          !  
 XXXXXXXXXX  !          !  +---------- chymo-laba (XX)  I  S  D  O
             !          !  !  
 XXXXXXXXXX  !          +-81         +-- batroxobin (S1)  I  S  D  O
             !             !  +-----11  
 XXXXXXXXXX  !             !  !      +--- ancrod (S1)  I  S  D  O
             !             +-18   
 XXXXXXXXXX  !                !  +-- trypsincod (S1)  I  S  D  O
             !                +-20   
 XXXXXXXXXX  !                   !  +-- trypIIhum (S1)  I  S  D  O
             !                   +-19   
 XXXXXXXXXX  !                      +-- tryp1hum (S1)  I  S  D  O
             !  
 XXXXXXXXXX  +-- brachyurin (S1)   I  S  D  O

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Go to the Department of Biochemistry and Molecular Biophysics

Thierry Rose, PhD and Enrico Di Cera, MD
Department of Biochemistry and Molecular Biophysics
Washington University School of Medicine
Saint Louis, MO, U.S.A.